Parameterization results
Atoms
|
RMSD |
Maximum deviation |
Average deviation |
Pearson2 |
Number of atoms |
| Parameterization | 0.0791 |
0.9498 |
0.0534 |
0.9592 |
122751 |
| Validation | 0.0854 |
1.1354 |
0.0565 |
0.9536 |
13639 |
Molecules
|
RMSD |
Maximum deviation |
Average deviation |
Pearson2 |
Number of molecules |
Smallest molecule atoms |
Largest molecule atoms |
Average number of atoms |
| Parameterization | 0.0741 |
0.2094 |
0.0546 |
0.9568 |
4027 |
5 |
124 |
30.482 |
| Validation | 0.0768 |
0.2173 |
0.057 |
0.9543 |
448 |
9 |
100 |
30.4442 |
Atomic types - Parameterization
| Atomic type |
RMSD |
Maximum deviation |
Average deviation |
Pearson2 |
Number of atoms |
% |
| Br | 0.0497 | 0.1384 | 0.0362 | 0.3917 | 273 | 0.22 |
| C | 0.0882 | 0.6738 | 0.0657 | 0.914 | 48311 | 39.36 |
| Cl | 0.0602 | 0.3194 | 0.0474 | 0.6744 | 984 | 0.8 |
| F | 0.0654 | 0.3082 | 0.0387 | 0.4371 | 818 | 0.67 |
| H | 0.0436 | 0.211 | 0.0305 | 0.6632 | 51411 | 41.88 |
| I | 0.0442 | 0.1701 | 0.0328 | 0.274 | 1555 | 1.27 |
| N | 0.1181 | 0.4946 | 0.0942 | 0.8747 | 7086 | 5.77 |
| O | 0.0887 | 0.4718 | 0.0628 | 0.8167 | 9784 | 7.97 |
| P | 0.3524 | 0.9498 | 0.2646 | 0.7798 | 349 | 0.28 |
| S | 0.1708 | 0.6045 | 0.137 | 0.9716 | 2180 | 1.78 |
Atomic types - Validation
| Atomic type |
RMSD |
Maximum deviation |
Average deviation |
Pearson2 |
Number of atoms |
% |
| Br | 0.0445 | 0.1572 | 0.0291 | 0.4934 | 63 | 0.46 |
| C | 0.094 | 0.5964 | 0.0683 | 0.8946 | 5351 | 39.23 |
| Cl | 0.0598 | 0.2686 | 0.0465 | 0.6846 | 100 | 0.73 |
| F | 0.0774 | 0.2201 | 0.0503 | 0.466 | 120 | 0.88 |
| H | 0.0489 | 0.2093 | 0.0338 | 0.6154 | 5708 | 41.85 |
| I | 0.0484 | 0.1316 | 0.0356 | 0.1798 | 179 | 1.31 |
| N | 0.1279 | 0.4432 | 0.0993 | 0.8746 | 793 | 5.81 |
| O | 0.0932 | 0.403 | 0.0643 | 0.7948 | 1025 | 7.52 |
| P | 0.3639 | 1.1354 | 0.268 | 0.7722 | 55 | 0.4 |
| S | 0.1791 | 0.5724 | 0.1406 | 0.9683 | 245 | 1.8 |
| Legend: RMSD |
< 0.05 |
< 0.1 |
< 0.15 |
< 0.2 |
< 0.3 |
< 0.4 |
>= 0.4 |
| Type |
Count |
% |
| C-H | 46451 | 36.81 |
| C-C | 43152 | 34.2 |
| C-N | 11170 | 8.85 |
| C-O | 8208 | 6.5 |
| H-N | 3301 | 2.62 |
| C-S | 2543 | 2.02 |
| O-S | 2019 | 1.6 |
| C-I | 1551 | 1.23 |
| H-O | 1438 | 1.14 |
| N-O | 1248 | 0.99 |
| N-N | 874 | 0.69 |
| C-Cl | 786 | 0.62 |
| C-F | 705 | 0.56 |
| O-P | 666 | 0.53 |
| C-P | 376 | 0.3 |
| N-S | 372 | 0.29 |
| Br-C | 245 | 0.19 |
| S-S | 226 | 0.18 |
| H-S | 206 | 0.16 |
| N-P | 199 | 0.16 |
| Cl-S | 121 | 0.1 |
| F-S | 109 | 0.09 |
| O-O | 91 | 0.07 |
| Cl-N | 77 | 0.06 |
| Br-N | 28 | 0.02 |
| H-P | 15 | 0.01 |
| F-P | 4 | 0.0 |
| I-O | 3 | 0.0 |
| P-P | 2 | 0.0 |
| I-N | 1 | 0.0 |
Set of molecules: DTP_large.sdf
Method: EEM
Optimization method: guided_minimization
Subset heuristic: 5
Samples: 500000
Minimization method: SLSQP
Date of parameterization: 2019-04-04 10:58
Time: 0:23:21
Number of cpu: 4
Command: ./mach.py --mode parameterization --method EEM --optimization_method guided_minimization --minimization_method SLSQP --parameters EEM.json --sdf DTP_large.sdf --ref_charges DTP_large.chg --data_dir results_data --cpu 4 --git_hash 2dc647db55f085e398df3be292a61ce3f46d7847 --atomic_types_pattern plain --subset_heuristic 5 --num_of_samples 500000 --validation 10
Github commit hash: 2dc647db55f085e398df3be292a61ce3f46d7847
Original parameters file
original_parameters.json
SDF file
DTP_large.sdf
Empirical charges file
DTP_large_EEM.chg
Reference charges file
DTP_large.chg
Molecules logs
molecules.log